Abstract：This study aimed to investigate the influence of the waterlogging on the photosynthesisof the cotton using a hyperspectral model based on the photochemical reflectance index (PRI) and fluorescence ratio index (FRI). A field experiment was performed on the cotton plants that subjected to four durationsof waterlogging with 1, 3, 6, and 9 days during flowering and boll-forming stage. The leaf reflectance, gas exchange, and chlorophyll fluorescence of the four leaves from the top of cotton plants were measured after waterlogging and following,as well compared with non-waterlogged plants. Results showed that：1) Net photosynthetic rate (Pn) decreased significantly after the 1th day of waterlogging, whereas the factors leading to Pn reduction varied with the duration of waterlogging. The ability of cotton to fixcarbon decreased significantly as the waterlogging duration less than 3 days. The stomatal factor was the principal factor leading to Pn reduction within 3-6 days of waterlogging, whereas the stomatal and non-stomatal factors were responsible for C fixation as the durationof waterlogging longer than 6 days. 2) After the 1th day of waterlogging, the significant decrease indices were the actual PSII photochemistry efficiency (ΦPSⅡ), apparent photosynthetic electron transfer rate (ETR), and photochemistry quenching coefficient (qP), whereas the increase in the non-photochemistry quenching coefficient (NPQ). After the 3rd day of waterlogging, the initial fluorescence (Fo) increased significantly, and the maximum photochemistry efficiency (Fv/Fm) decreased after the 6th day of waterlogging. Showing that PSⅡreaction center of the cotton leaves was destroyed by waterlogging, where the transfer rateof electrons and its efficiency were significantly reduced, leading to the decrease in the conversion rate of light energy, as well the distribution part of light energy that absorbed by PSⅡ antenna pigments for photochemistry electron transfer, whereas the part that consumed by heat increasedsignificantly. Under the waterlogging stress, the share of light energy that used to photochemical reaction, share(P) was reduced significantly, while the invalid dissipation(the light energy share used in antenna heat dissipation(D) and used in PS Ⅱ reaction center non-photochemical dissipation(E)) significantly increased, resulting the decrease in the utilization efficiency of light energy. There were strong non-linear relationships between the durations of waterloggingwith the increasing rate of D and E, and the reduction rate of P. 3) The PRI values decreased significantly, while FRI=R600 / R690 and FRI=R740 / R800 increased significantly after the 3rd day of waterlogging. Under the waterlogging during the flowering and boll-forming stage, the PRI, FRI=R740/R800, FRI=R740/R800, gas exchange parameters, chlorophyll fluorescence parameters demonstrated a linear relationship, indicating the hyperspectral models were feasible to predict the dynamic effects of the waterlogging damage on the gas exchange and chlorophyll fluorescence of the fourth leaf from the top of plants. By comparison, the hyperspectral models were verified by high precision on simulating Pn and Gs dynamics in gas exchange and Fo, Fv/Fmand NPQ dynamics in chlorophyll fluorescence. The determination coefficient (R2), normalized root mean square error (NRMSE) and sensitivity of spectral parameters to waterlogging have confirmed that the established hyperspectral model involving PRI are suitable to simulate Pn, Gs, Fo, Fv / Fm and NPQ during the short-term waterlogging duration at the late reproductive growth period of cotton plants.